Disqus - Latest Comments for Pedro Beltrao

Re: Is it enough to study individual molecules?

Pedro Beltrao — Thu, 01 Jun 2006 16:04:33 -0000

Just thought you might enjoy reading or re-reading this opinion about a somewhat exaggerated emphasis on interdisciplinary teams.

Re: Things I noticed #8

Pedro Beltrao — Sun, 08 Oct 2006 10:04:50 -0000

Pierre from YAKAFON also made an interesting Google gadget.

I really like the ideas around the Amazon scalable IT products. They also rent out processing power with their EC2 product. Sun also has a grid service for anyone interested on scalable processing. This goes in a trend of outsourcing the IT department. Instead of having to manage servers on your company/research institute maybe it makes more sense to rent it as need arises from someone. Maybe for private owners it is still early but for most medium size groups this is likely a good option right now.

Maybe we should try to right a wiki review :) the problem is that we are all from slightly unrelated fields.

Re: Biological content: Access and monetization

Pedro Beltrao — Thu, 09 Nov 2006 11:44:39 -0000

I am compiling data on known phosphorylation sites in human proteins. Yesterday I went trough a paper that had in supplementary materials a list of phosphorylated sites linked to proteins via IDs. They used 3 different ID types in the same field that I had to parse to my own favorite human id. I then downloaded a database that was at least well formated (in XML) but I still had to match their own ID to the one I was interested by blasting the protein sequences ... I sill have at least two more databases to go.

How I wish that there were a more standardized form of communicating scientific data. It is more important that we spend resources thinking of what to do with the information than on how to get it all together.

Re: Spreading a meme

Pedro Beltrao — Wed, 22 Nov 2006 09:57:28 -0000

After a while the 2.0 gimmick becomes a bit too much. It is a very successful meme. Here is for example a podcast about Library 2.0
I have been trying to say open science instead of science 2.0 to mean a more transparent scientific process and not just open access that refers to accessibility to the papers.

Re: Google Reader trends

Pedro Beltrao — Fri, 05 Jan 2007 14:09:59 -0000

Happy new year :)
I can say that you consume more than 10 times more posts than I do ;)
There are a couple of useful features to help to remove some feeds from the list but in the end this looks more interesting for marketing or ad networks.

Re: Pedro blogs a paper

Pedro Beltrao — Tue, 09 Jan 2007 04:32:52 -0000

Thanks :). I also get the same feeling that blogs help to put a human face on a scientists. I think that is a good think. If more people did this, it would make it easier to ask questions to the authors and to establish working ties with others. The only possible negative side effect could be that we might be more subjective towards the research we read.

To bad that Gerstein does not allow comments on his blog :).

Re: “Social” science

Pedro Beltrao — Tue, 23 Jan 2007 06:53:13 -0000

I should have really stressed more that I am not really familiar with text mining :).
It is interesting to think of sub spaces in the social web. If had tried to do this in delicious I would probably get a very different result since Connotea is much more focused on science and annotation of science papers. In a way the ideal situation would be to have a global tag space but more information on the taggers. One could decide to use or not the tags according the individual's knowledge base.

Re: Talking open science at Ignite Seattle

Pedro Beltrao — Sun, 04 Mar 2007 10:53:51 -0000

That was fun to watch :). A lot of hiccups with the slide changes but overall a very cool presentation.

Re: Journal clubs on PloS One

Pedro Beltrao — Sun, 11 Mar 2007 09:12:05 -0000

That is an interesting possibility. They could go in the direction of a social network. Right now however I think it would be more useful to have some sort of gateway system per topic of interest. The landing page is just not enough as a place to explore the content in PLoS ONE.

Re: Google acquires Gapminder software

Pedro Beltrao — Fri, 16 Mar 2007 20:54:48 -0000

:) When I read the news I thought you would find this interesting. I hope they find a way to integrate this with their spreadsheet app.

Re: Science in silico

Pedro Beltrao — Sat, 21 Apr 2007 10:02:42 -0000

That looks cool :). Visualization is a tricky business. It really helps up think but at the same time it can also trick us by miss representing reality. In the end these are models and it is so easy to look at these amazing pictures and reason with them forgetting than they are our best guess.

I was thinking about visualization recently in the context of signaling. I can't really grasp how cells compute signaling events. It is so diffuse and apparently chaotic with so many shared components between different pathways, that I can't find a good analogy to visualize signaling. Protein complexes are easier, they are these machines with 3D shapes and movement. Some of the components might change, but that is still easy to visualize. It would be cool if someone would come up with an easier way to visualize signaling inside cells.

Re: Life science venture funding goes up

Pedro Beltrao — Wed, 25 Apr 2007 08:12:49 -0000

This is good news. Maybe this will translate in more biotech jobs too :).

Re: The big get bigger, but there is so much more

Pedro Beltrao — Fri, 18 May 2007 09:03:47 -0000

I really don't buy into this idea that the net is shrinking.The sites mentioned Wikipedia, MySpace are expanding and have a very high turn-over. Even we are focusing on a narrower range of domains this does not mean that it is not easy for anyone to get a voice online. On the contrary it has never been so easy to start a webpage connect yourself to group of related pages to a point were you build up an audience. It is as easy as starting a blog and setting up a blogroll. Most likely the links will attract the attention of fellow bloggers and other readers of these blogs.

Re: Computing in the cloud

Pedro Beltrao — Sat, 02 Jun 2007 08:25:44 -0000

That is really cool. It really depends on the costs but factoring in the IT support it might very well pay off for many research institutes.

Re: Science, blogs and data

Pedro Beltrao — Sun, 10 Jun 2007 06:59:17 -0000

A part of the challenge is also getting the blogging platforms to have easy microformat tools. It has to be trivial to use. For example when linking to a manuscript or book the blogging tool could recognize the work and ask for for metadata, writing down the result in text and in hReview. The same for other types of data. A small button to add interaction data to the blog post, things like this.

Re: Bringing the wisdom of crowds to peer review

Pedro Beltrao — Tue, 10 Jul 2007 15:23:23 -0000

I like the insight part. How would we rate the usefulness of something like the discovery of RNA interference (just to give an extreme example) ? When we read it we know that it is something that other people should read, even it I am not going to use it immediately for my work. Sometimes we just want to say how far reaching this discovery can be and go tell the world about it. Some other times we can find it useful for a very small niche area. So I think the perceived impact, that comes before the use (although directly connected) is also important. We rely on impact factors for this today, but it would be better to evaluate the impact of individual papers from user ratings and of course usage values and citations.

Re: The Lijit Wijit

Pedro Beltrao — Thu, 12 Jul 2007 08:54:24 -0000

It is probably also a good way to find things that you know you read but not quite sure where. thanks for the trust :)

Re: Knowledge discovery via Lijit

Pedro Beltrao — Sun, 15 Jul 2007 08:17:04 -0000

It looks like Blogger on draft is now providing a similar search feature. It automatically creates a Google Custom search from the blog content and what we linked. This is an interesting direction for people powered search. I am not sure how, but this could then feedback to the main Google search.

Re: Scifoo: Google and large scientific datasets

Pedro Beltrao — Fri, 10 Aug 2007 05:06:34 -0000

This is really interesting. I remember hearing about it somewhere about how they were storing scientific data for NASA or something of this sort but I did not know they were planning to expand this and make it available to all.

Re: Nature.com gets a facelift

Pedro Beltrao — Tue, 14 Aug 2007 20:57:21 -0000

Postgenomic missing - Here is a speculation ... they might want to keep postgenomic as independent (unbranded) as possible to be used by several publishers.

Re: SciVee.tv

Pedro Beltrao — Mon, 20 Aug 2007 04:30:46 -0000

This is an interesting twist. Nature is mostly developing in house their new tools but maybe collaborating with start-ups would be an alternative way of building tools for publishers. The publishers provide the people (social graph) and content and the start-ups provide the tools.

Re: Account issues

Pedro Beltrao — Tue, 21 Aug 2007 07:01:08 -0000

It was about 5 internet years ;) Google bought Yahoo in the meantime.

Re: More Second Life goodness

Pedro Beltrao — Wed, 05 Sep 2007 10:34:30 -0000

They should let us have our names instead of those nicks if we wished too. Next time I will know your nick. I am not sure I will attend the next one since I will be away in a conference but I can try.

Re: Your personal health: The dirt on 23andme

Pedro Beltrao — Fri, 14 Sep 2007 10:58:26 -0000

I just hope that the hype will not grow to a point were people forget how much the environment shapes the outcomes. When the "Craigome" came out in PLoS Biology all the sound clips in CNN were about how much we will be able to predict from our genomes etc. To make any sense of the SNP data a lot of cultural habits, diet information, etc will have to be collected as well. How comfortable will people be in centralizing this much information in a private company ?

Re: Connotea for physicians

Pedro Beltrao — Thu, 27 Sep 2007 05:00:48 -0000

What I don't like about this fragmentation (specialization) is that these social sites work better the more people participate in them. So, the more fragmented the space the harder it will become to reach interesting levels of users. In all these social sites it would be best if the underlying important material would be shared, accessible to any other site. The competition between the sites could be on the user interface and not so much on who has the most tagged material or largest social network etc. I guess in tagging there are clear advantages to specialization. I don't want to go through all material in delicious if I am looking for new papers for example.

Re: Why are we MD types so closed?

Pedro Beltrao — Thu, 27 Sep 2007 05:07:33 -0000

Now that they have ONE I don't know if they will open new journals any time soon :). More likely they will create portals based on the content in PLoS ONE. You can always try to create a journal in BioMed Central.

Re: The future of PLoS - Community and science

Pedro Beltrao — Sat, 29 Sep 2007 06:30:24 -0000

I could not find the comment but to be clear what I think is that they will not launch new journals any time soon since they will probably be focusing on this re-grouping of content.The Hubs are not journals in the sense that we don't submit the manuscript to the Hubs. I hope they find some time and man power to allow for more user generated content in the Hubs. Some kind of "editorial" boards that can post the editorials and some Hubs that are created by the users. Some cross between Nodapoint, Digg and Nature Reports.

Re: JournalFire: Online journal clubs

Pedro Beltrao — Thu, 11 Oct 2007 05:45:46 -0000

The first time I checked the site it only allowed .edu email addresses. I sent an email asking for an account saying that I was in EMBL (embl.de) so I think that they are adding upon request. They also changed the login for invitation only so even if the domain is now accepted I can't create an account :).

Re: Venture investment by industry

Pedro Beltrao — Sat, 13 Oct 2007 11:59:11 -0000

I will be moving to SF next year. One thing that I had in mind for the next years while I do the posdoc would be to find some way to get in touch with biotech people in the area. I like the academic world but I would at least like to understand better the potential and limitations of working in biotech.

Re: A different kind of social network

Pedro Beltrao — Thu, 18 Oct 2007 09:28:26 -0000

Don't forget how the group got that big ;). In any case it is difficult to get the average person to participate in most online activities. I remember an observation that someone made about the 1% rule of social sites. Only about 1% of people are active in most of these sites. I don't remember where I read it and this estimate could be off by now. Some sites are better than others in stimulating participation. Facebook is so far the best example from those that I have tried.
Going back to the questions. Aside from having a discussion on the daily challenges in bioinformatics as suggested by Keith and Neil in Neil's blog I would be interested also in some historical perspective from someone that has been in the field for a long time (ex Philip E. Bourne).

Re: The value of information

Pedro Beltrao — Thu, 18 Oct 2007 11:35:23 -0000

There are always differentiators. Just the fact that you are the fist to develop a new method in the lab, even if you fully describe the method when you publish it your still in the leading edge and that gives you an advantage in working with that method or in making improvements.
I don't really agree with that idea that once everyone known something that there is no longer a competitive advantage in knowing that. No person can know everything and what a person or group does with that shared public knowledge is strongly dependent on the groups background. I think that in a very open world of knowledge it becomes increasingly difficult to be original as an individual because it is likely that someone out there has the same knowledge and mindset and ideas. However, as a sum we should be collectively more creative. There are many more different melting pots and discussions over this shared knowledge.
Even the simple act of having open discussions about this shared knowledge can be of value. We can learn how to argue our positions, to spot weaknesses in logic etc from observation.

Re: Science continues to get more social

Pedro Beltrao — Tue, 27 Nov 2007 14:20:06 -0000

I had a quick look around but nothing grabbed my attention. The groups idea is nice but I prefer JournalFire or Scintilla. They could consider importing tagged data from Connotea and Citeulike to bootstrap it. I wonder if they can do this.

Re: Bursty work

Pedro Beltrao — Fri, 21 Dec 2007 14:41:48 -0000

For science I think this "bursty work" is an excellent concept. To establish collaborations we are still very limited on the people around us in the institutes, the contacts we make in meetings or from our current/previous supervisors (real life stuff). I was just trying to set up a bioinformatics/evolution project in Google Code and in just a few weeks I got at least two other researchers interested in collaborating and a few others asking questions and correcting a few mistakes. I think trying out research ideas this way is very different from having a group leader thinking about a project and trying to sell it to the next PhD student or postdoc coming to the lab.

Re: Why I have a problem with BPR3

Pedro Beltrao — Thu, 24 Jan 2008 20:59:38 -0000

I'll be repeating myself but what I don't like about BPR3 has more to do with fragmentation of attention. It would be great to have a place like techmeme for science where a large fraction of science bloggers, scientists and maybe even journalists would read about the latest science news. The more aggregators there are the harder it will be to have a large network effect kicking in.

Re: The future of scientific collaboration: Extending the “Bursty Work” concept

Pedro Beltrao — Thu, 07 Feb 2008 13:44:46 -0000

We might need slightly better tools to organize the projects but the critical aspect is right now is awareness. It would be great to be able to start a project and state the needed resources (people/skills/materials/etc). This should trigger an alert to anyone willing to provide this. Something like an RSS feed that I could subscribe to for tags that qualify the resources that I am willing to provide currently. This could slowly move the research agendas from the physical local institutes and universities to the web.

Re: Continuing thoughts on innovation models

Pedro Beltrao — Thu, 24 Apr 2008 19:15:03 -0000

A slightly different angle is that the problems/big questions that can be more easily tackled given current technologies and foreseeable advances are not readily accessible. Exciting and clearly stated research agendas would attract this distributed research environment.

Re: Google Code as a science repository

Pedro Beltrao — Thu, 22 May 2008 13:29:42 -0000

That reminds me that I still did not make time to push on that open project ... hopefully when I get one project done in the new lab I will have an easier time convincing the boss that this is OK.

Re: New Facebook: Twitter + FriendFeed + 175 million users

Pedro Beltrao — Wed, 04 Mar 2009 20:39:47 -0000

Actually Friendfeed is very usual (in contrast to Twitter). I am working in academic research and I use FriendFeed to keep track of what other researchers are reading and to participate in scientific discussions. I have seen many examples where it was helpful to solve problems in much the same way a forum would. There are currently around 640 scientists registered in the "The Life Scientists" friendfeed room.

Re: 2006/02/12/3bubbles-why-im-skeptical-about-live-chat-on-blogs/

Pedro Beltrao — Sun, 12 Feb 2006 14:52:26 -0000

what about for the ability to chat with the blog owner. A lot of bloggers spend a considerable time online. Sometimes it would be more interesting to chat with the blogger instead of just posting a comment and coming back some time later for the answer.

Re: So long 26th grade!

Pedro Beltrao — Tue, 07 Apr 2009 23:09:08 -0000

Congratulations Dr Good :)

Re: my cloudy evolution

Pedro Beltrao — Wed, 05 Aug 2009 16:34:56 -0000

Maybe you should not put publishers out of the picture all together. There might be some of them that are willing to create the team that has sort the freedom to think outside of the document mentality.

Re: Sitting here with Buzz talking about Google’s Zeitgeist conference

Pedro Beltrao — Fri, 28 Oct 2005 06:10:28 -0000

This is even worse than not saying anything :) now I am curious. "We cannot blog about, except to say that it was amazing and I saw and heard fantastic things that I cannot share with you ..." oh well :)

Re: Interesting, don’t miss second page

Pedro Beltrao — Sat, 29 Oct 2005 14:03:48 -0000

Why call it attention and not identity ? And why keep it only in the web. Any portable device can carry your identity anywhere you go in some kind of wifi radius thingy. Get into a bar and have the bar music player mesh your music preferences into the playing list. Social music mesh up in the real world. The barmen offers you a menu built on your possible preferences. Are you flying to Brazil next month ? Here try this drink.

Re: Arrington, at TechCrunch, likes the MSFT gadgets the best

Pedro Beltrao — Wed, 02 Nov 2005 08:08:09 -0000

Now .. if they (amazon, ebay, google, yahoo, MS, etc) all got together and agreed to merge their identifiers. I hate having to log in to all of these. Make it really about innovation and not about who can grab my attention and my data and lock me into their services.

Re: More disruption from Google: it’s patenting attention data display

Pedro Beltrao — Thu, 03 Nov 2005 10:23:15 -0000

I said so before in a previous comment here in the blog. This is a very important point. My identity/attention data should not be locked inside a particular service provider. This results in a rich-get-richer model that will lead to a clear winner and no competition. Much in the same way that no particular company should own the OS platform cof :)

Re: Sam Ramji opens SaaS program at Microsoft

Pedro Beltrao — Fri, 04 Nov 2005 13:09:34 -0000

And no comment on the Mechanical Turk thing over at Amazon yet :) ? Amazon's very own monetizing gadget ?

Re: Google Reader + Facebook Application = Digg killer?

Pedro Beltrao — Sun, 15 Jul 2007 13:53:39 -0000

It could also be the stared items if we make them public. This is how I usually mark the posts I like in GReader.
I get the general interest. It goes into making group certification of content a lot easier. An abstraction of techmeme to any group of people. The great thing is that there are much more readers than bloggers that can come in and contribute with the editorial capacity without having to post to direct attention. It also helps to separate the two main functions of the blog, creating content and directing attention.